Not As He Seems
by yaystories1245
Summary: Based on a Tumblr prompt: A superhero story where the superhero and villain are roommates and they keep making excuses to each other about why they are out all the time and they stitch each other up after battles, but neither has any idea that the others their nemesis and they keep on having to lie to each other why they are covered in scratches and bruises.
1. Chapter 1

**AN: HI, look who's back, I'm not dead! Yes, I have come back to present you with a new story. I hope you'll all enjoy.**

 **Disclaimer: I do not own The Maze Runner trilogy or any characters mentioned in this story. I only own the story.**

"Newt?" Thomas called as he opened the door to their shared apartment. He didn't expect him to be home, he barely ever was, neither of them were home very often. Thomas gave a halfhearted smile and removed his laptop from his backpack, tossing the backpack aside and made his way into their living room. At least without Newt here he could get some work done. Newt was like an overactive puppy, always seeking attention. Not that Thomas minded, he'd grown quite fond of Newt. His heart fluttered at the thought of the blonde. He smiled fondly and plopped down on their couch.

He opened his laptop and tried to start on his research paper. He felt he was finally getting somewhere when he heard the door open. "Tommy, I'm home!". The blonde's voice filled their home, bringing a smile to the brunette's face. "I'm in the living room!". Newt made his way into the living room, dumping his backpack on the floor near the plopped down on the couch and placed his feet in the crease between couch and Thomas' back. "So, whatcha doin'?". Thomas smirked, eyes never leaving the screen of the laptop, "Were you watching Phineas and Ferb on the way home again?" Newt gave a lopsided grin, "It's a possibility.". Thomas gave an amused grunt, "How old are you?" "Approximately one year, three months and six days older than you." "Whatever." "So what are you actually doing?" "Research paper." "Boooo.". Thomas chuckled, briefly glancing up at the blonde, "Well Newt, some of us actually have important things we need to get done." "Well excuse me Mr. Undergrad, but not all of us can be in medical school, and as a matter of fact I do do important things." "Oh yeah, like what?" "Need I remind you I major in mechanical engineering?" "Which makes you an Undergrad, too.". Thomas said interrupting Newt's rant. "As I was saying before I was so rudely interrupted." Newt said, earning a snort from Thomas. "I had to build a robot for Mr. Janson's class and I go an A." Newt said sending a smug grin in Thomas' direction.

Thomas rolled his eyes. "Then how come I never saw you working on this supposed robot." "That's because I do all my important projects at the library, where there are no distractions or interruptions." Thomas gave a halfhearted nod, eyes never leaving the screen. "You should do your projects at the library, too." Newt suggested. "Besides it doesn't look like you're getting much done here." That had caught Thomas's attention, tearing his eyes away from the screen he finally looked up, looking almost offended. "I have to gotten some work done!" "Oh yeah, how much?" Thomas looked down, trying to shield the computer screen from Newt. "A couple of sentences." Thomas mumbled. "What was that Tommy, I didn't quite catch that?" Newt said, sending a suggestive smirk his way. Thomas sneered at him "A couple of sentences.". Newt didn't even try to conceal his laughter all the while Thomas glared daggers at him. "Shut it, Salamander." "Aw come on Tommy, you know you love me. I'm serious though, you should really consider my suggestion.". Thomas had to laugh at that. "Could you imagine us in a library?" Newt snorted. "It'd be the best thing ever." Thomas didn't even try to conceal his smile. "So Tommy, are you going to sit there on your arse all day and pretend to get work done or are you going to allow me escort you to our local library?" Newt said standing up and offering Thomas a hand, "Shall we?" Thomas took Newt's outstretched hand, closing his laptop and tossing it aside "We shall."

 **AN: First chapter is done, hope you guys enjoyed it. I apologize for any grammatical errors, it's 12 am here and I was listening to Fall Out Boy, so I was a little distracted. I've already started working on the second chapter, so that should be up soon. If you have and suggestions I'd love to here them. Until next time Merry Christmas Eve.**


	2. Chapter 2

**AN: I'm so, so, so ,so, sorry! My laptop crashed and then I had to get it fixed and then school and I'm really sorry! But hey, second chapter is here, and it's longer than my first chapter. I'm working on making longer chapters, so that's something to look forward to. Anyways, let's get this show on the road.**

 **Disclaimer: I do not own The Maze Runner trilogy or any characters mentioned in this story. I only own the story.**

Thomas and Newt made their way out of their apartment, hands still tightly clasped together. "Well look who it is, lovebirds, how ya been." Newt and Thomas snapped their heads in the direction of the voice. Newt's eyes lit up upon seeing the owner of the voice.

"Minho!" Newt released Thomas' hand to give the Korean a hug. Thomas missed the warmth that Newt's hand had supplied almost immediately.

"So where is my favorite couple headed." "One, we're not a couple, two I'm escorting Tommy here to the library, so he doesn't flunk out of med school." Thomas punched Newt lightly in the arm. "I wouldn't have flunked out, dummy." Newt ruffled Thomas' hair at the comment which resulted in Thomas batting at Newt's hands trying to remove the blonde's hands from his hair. "Aww Tommy you're adorable."

Minho fonded at the pair as he watched the exchange. "Oi, Min, what are you staring at?" Newt asked, his arm lazily draped across Thomas' shoulders. "Oh nothing, nothing." Minho said, suddenly finding the ceiling very interesting.

"Don't you two have somewhere to be?" "Oh yeah Newt we better go." Thomas said shrugging Newt's arm off his shoulders. "See ya Min." Newt said as Thomas grabbed his hand and dragged him along behind him. Minho chuckled as he watched the retreating figures, they were so oblivious, he'd have to fix that.

"Tommy, do you really think you should be dragging me, you don't even know where you're going." Newt smirked at the brunette as he slowed his pace.

"I don't care for your suggestions, Newt." Newt rolled his eyes at the brunette, "Okay Tommy, but don't come at me with your bloody accusations when we get lost or worse {EXPELLED}* mugged." "We're not going to get lost, trust me."

Newt and Thomas were definitely lost. Newt was sure they had passed this same restaurant three times now and the sun had gone down long since they had left the apartment.

"Tommy, admit it, we're lost" "We're not lost Newt, I already told you I know exactly where we're going." Newt made an abrupt stop in the middle of the sidewalk, and grabbed the hood of Thomas' jacket, pulling him back. "You and I both know that you don't know where we are, bloody hell Thomas, I don't even think I've ever been on this side of town before!"

Thomas stopped and turned towards Newt, he could see the obvious frustration in the blonde's eyes. Thomas gave a lopsided grin, trying to lighten the mood "What could go wrong?" "Oh, I think plenty of things could go wrong." Thomas and Newt froze, the unfamiliar voice shocking them, they looked into the alleyway and saw two figures slowly approaching them.

"Newt." Thomas whispered "Newt, run." "Tommy, what?" "Newt, RUN!" pushing Newt in the opposite direction, he took off in a sprint, he knew who could help he just hoped he could run fast enough.

Newt should've known as soon as Thomas had asked him "What could go wrong?" That something bad was going to happen. Newt probably shouldn't have trusted Thomas in the first place, look where that had gotten him. Running as fast as he could, or as fast as anyone with a limp could.

"If we make it out of this alive, I'm going to kill Thomas." newt thought as he heard his pursuers' footsteps not too far behind him. Newt thought he was making progress, he could keep this up long enough to find help, or that what we would've been thinking if he hadn't just tripped.

Newt cursed out loud as his shoulder took the impact of the fall, he thought that if there had been anyone around they would've definitely heard him. He heard his pursuer slow to a stop and give a dark chuckle as he saw the crumpled body on the ground that was newt.

Newt wished his legs weren't completely useless as the man kicked him in the ribs, newt held in a grunt even though it hurt like heck. The man chuckled again as he repeatedly kicked newt in his rib cage, "That's gonna leave a bruise or two." Newt thought as the man sent another kick into newt's ribcage.

The man kneeled down next to newt so he could hear him loud and clear, "Oh how the mighty have fallen, you aren't so high and mighty now without your little friend, what did you call him, Tommy, I believe it was." A hot, fiery rage burned in Newt's core "You don't get to call him that." Newt's assaulter leaned in closer "Sorry, didn't quite catch that." "Only I can call him that."

The man gave a hearty laugh and yanked newt up by his jacket and slammed his back against the brick wall. "One more time Gecko." A sinister tone to the man's voice. Before newt had a chance to respond, however, a body slammed into Newt's assaulter taking the man down to the ground.

Newt slumped down the wall a little bit and closed his eyes. "About time, Tommy." newt thought as the fight continued on. When newt finally opened his eyes the fight seemed just about over, what Newt hadn't been expecting was that he had been saved by the acclaimed superhero of their small city, Night Hunter.

Newt scowled, he absolutely loathed the superhero. Newt was offered a hand up, but pushed it away, standing on his own. Newt winced as his shoulder ached in protest, he clutched it hoping that would stop the pain or at least dull it and started to make his way past the superhero. "Wait, I think you need medical attention." Newt rolled his eyes "Thanks Captain Obvious, but I don't need your medical opinion, I need to find my friend."

Newt made his way back onto the sidewalk, where he had last seen Thomas. "Tommy?!" Newt called looking around. "Newt!" Newt turned around to see Thomas coming at him from the way he had just come from.

Newt's heart swelled at the sight of the brunette and he seemed okay, even better. Thomas ran up to newt and encased him in a tight hug, newt winced, the action irritating his injuries. This didn't go unnoticed by Thomas, "Hey, are you okay, did they hurt you?" Newt chuckled, earning him another wince and a worried glance from Thomas. "Just a little bruised, don't worry about it Tommy."

"Gosh newt I'm so sorry, this is all my fault." Thomas said looking sheepishly down at his shoes. "Hey, hey Tommy look at me, okay I'm fine a little bruised up at most, okay, so don't sweat it." Newt reassured bringing the brunette in for another hug.

"When we get back I'm giving you a full checkup, okay?" "Yes, doctor." newt chuckled and slung an arm around Thomas' shoulder as the brunette pulled out his phone to use his GPS to get them home.

"Well it looks like you're ribs are bruised and then you just have a couple of bruises on your back and shoulder." as he examined Newt's bare back and torso. "Oh doctor, how will I ever recover?" Newt asked in the most dramatic way possible, making Thomas giggle. "Ice for the bruises on your back and shoulder, for your ribs you'll need to take pain meds and ice every 15 to 20 minutes 3 to 4 times a day, and lots of rest."

"Wow Tommy, who knew you were actually good at this medical crap." Thomas blushed at the comment. "It's pretty simple stuff actually, it's not like I actually really did anything." "Well I appreciate it anyways." newt smiled looking into Thomas' eyes.

They stayed that way for a while, looking into each other's eyes until Thomas coughed suggesting newt get to bed and he'll bring him his ice. Newt looked almost disappointed, but complied saying he wouldn't argue with "doctors' orders". Thomas shot one more smile at the blonde before he disappeared beyond the threshold that separated the living room from the hallway into his room for some much needed rest.

 **AN:** So if you haven't already figured it out Thomas is the superhero and Newt is going to be the villain, but we'll get to that later.


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